SMTL ID : 8w9w.1

The cryo-EM structure of human sphingomyelin synthase-related protein in complex with ceramide/phosphoethanolamine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x UJO: ~{N}-[(~{Z},2~{S},3~{R})-1,3-bis(oxidanyl)heptadec-4-en-2-yl]dodecanamide(Non-covalent)

UJO.1: 14 residues within 4Å: Chain A: F.20, T.23, G.65, M.66, C.69, M.93, F.97, R.100, I.136, F.140, M.142, D.152, H.158, V.161 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.20, A:F.20, A:T.23, A:I.136, A:F.140, A:V.161 Hydrogen bonds: A:D.152 UJO.3: 13 residues within 4Å: Chain B: F.20, T.23, G.65, M.66, C.69, F.97, I.136, F.140, M.142, D.152, G.157, H.158, V.161 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.20, B:F.20, B:T.23, B:I.136, B:F.140, B:F.140, B:V.161 Hydrogen bonds: B:D.152 UJO.5: 16 residues within 4Å: Chain C: F.20, T.23, S.24, M.27, E.62, G.65, M.66, F.97, R.100, I.136, F.140, G.141, H.148, D.152, H.158, V.161 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.20, C:T.23, C:E.62, C:I.136, C:V.161, C:V.161 Hydrogen bonds: C:D.152 UJO.7: 12 residues within 4Å: Chain D: F.20, E.62, G.65, M.66, C.69, F.97, R.100, F.140, D.152, G.157, H.158, V.161 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.20, D:F.20, D:E.62, D:F.97, D:V.161 UJO.8: 13 residues within 4Å: Chain E: F.20, E.62, G.65, C.69, F.97, R.100, I.136, F.140, H.148, D.152, G.157, H.158, V.161 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:F.20, E:F.20, E:F.140, E:V.161 Hydrogen bonds: E:D.152 UJO.9: 16 residues within 4Å: Chain F: F.20, T.23, S.24, M.27, E.62, G.65, M.66, C.69, F.97, R.100, I.136, F.140, G.141, D.152, H.158, V.161 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:F.20, F:F.20, F:T.23, F:E.62, F:I.136, F:V.161 Hydrogen bonds: F:R.100, F:D.152

4 x OPE: PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER(Non-covalent)

OPE.2: 7 residues within 4Å: Chain A: M.27, R.132, I.136, V.147, T.149, C.150, G.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.150, A:G.151 OPE.4: 6 residues within 4Å: Chain B: M.27, R.132, I.136, V.147, C.150, G.151 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.150, B:G.151 OPE.6: 4 residues within 4Å: Chain C: V.147, H.148, T.149, C.150 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.149, C:T.149, C:C.150, C:C.150 OPE.10: 3 residues within 4Å: Chain F: V.147, T.149, C.150 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:T.149, F:C.150, F:C.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, K. et al., Cryo-EM structure of human sphingomyelin synthase and its mechanistic implications for sphingomyelin synthesis. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-02-28

Peptides

Sphingomyelin synthase-related protein 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Membrane

We predict this structure to be a membrane protein.
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Sphingomyelin synthase-related protein 1

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